arXiv subjects

Tjaart P. J. Krüger

Publications and source records attributed to Tjaart P. J. Krüger.

14 recordsLinked to original sources

arXiv2026

Body-of-Revolution Finite-Element Model of Plasmon-Enhanced Fluorescence

Plasmon-enhanced fluorescence (PEF) is one of the most widely investigated optical phenomena in hybrid systems of emitters and plasmonic nanoantennas, with applications ranging from biosensing to single-molecule emission microscopy. In this work, we extend finite-element modelling of PEF beyond spherically symmetric geometries using a body-of-revolution finite-element method (BOR-FEM). By exploiting exact or equivalent rotational symmetry, 3D emitter-nanoantenna systems are reduced to computationally efficient 2D formulations while retaining the essential electromagnetic interactions governing excitation and emission. We validate the framework against three previously investigated emitter-nanorod systems, including one requiring an equivalent axisymmetric geometric transformation, before applying it to an emitter-core-shell nanorod system. Specifically, we investigate the PEF of the terminal chlorophyll emitter of the major plant light-harvesting complex (LHCII), the most abundant membrane protein on Earth, interacting with a gold core-dielectric shell nanorod with one or two dielectric shells. The simulations reveal that the interplay between excitation enhancement, radiative-rate enhancement, and non-radiative Ohmic losses gives rise to four distinct shell-thickness-dependent operating regimes (quenching, enhancement, suppression, and decoupling), with recovery of the intrinsic quantum yield in the decoupling regime. The predicted enhancement factors for experimentally relevant dual-shell nanorods agree well with previously reported measurements. These results establish BOR-FEM as an efficient and versatile framework for modelling PEF in rotationally-symmetric nanoantenna geometries and in non-axisymmetric geometries that admit equivalent axisymmetric representations, providing a practical route for the rational design and optimisation of plasmon-enhanced bio-nanophotonic systems.

physics.optics↗

arXiv2026

Multipolar and nonlocal effects in plasmon-mediated entanglement generation

The generation of quantum entanglement is important for a wide range of quantum technology protocols. In nanophotonics, a promising platform for quantum technologies, entanglement generation via plasmon-mediated coupling in quantum dot qubits is often modeled within the dipole limit, where only dipolar plasmons of the mediating nanoparticle are considered, and the local response approximation, where nonlocal corrections are ignored. However, multipolar effects manifest strongly at coupling distances less than the nanoparticle size, while nonlocal optical effects stem from a size-induced dielectric response. We investigated these two important effects in the generation of two-qubit entanglement mediated by plasmonic coupling. A cavity quantum electrodynamic approach is employed, where the induced plasmonic effects lead to modified transition rates in the dynamics of the coupled quantum dot qubits. We find that multipolar modes and size-dependent damping lead to entanglement decay at small coupling distances and limit mediated entanglement with certain particle sizes. We discuss potential implications of multipolar modes in entanglement-based quantum sensing.

quant-ph↗

arXiv2026

Stationary two-qubit entanglement mediated by one-dimensional plasmonic nanoarrays

Entanglement is one of the key measures of quantum correlations present in nanophotonic systems, with promising applications in quantum optics and beyond. Previous studies have shown that the degree of entanglement between two quantum dot qubits is preserved when a metal nanoparticle is used to mediate the interactions between the qubits. In this work, we investigate long-range plasmonic mediation of qubit--qubit entanglement by studying the impact of the number of mediating metal nanoparticles on stationary concurrence. Collinear and periodically spaced metal nanoparticles that satisfy the weak-coupling approximation are considered. An effective model that enables the derivation of the mediated interactions within the framework of cavity quantum electrodynamics is employed. Under weak driving at the single particle resonance frequency, the model shows that odd-number arrays are more robust to entanglement decay. We attribute this to strong inter-qubit dissipative coupling as a result of a hybridized dipole plasmon resonating with the driving frequency in odd-number arrays. These arrays can sustain non-vanishing stationary entanglement beyond an inter-qubit spacing of one micron, opening up the possibility of independent spatial optical probing of each quantum dot.

quant-ph↗

arXiv2026

Size-Dependent Fluorescence Kinetics Reveal Contributions of Intrinsic Quenching and Singlet-Triplet Annihilation during LHCII Aggregation

Aggregation of the main antenna complex of higher plants, Light-Harvesting Complex II (LHCII), is widely used as an in vitro model for energy-dependent quenching (qE), yet fluorescence reduction in aggregates is frequently interpreted without a quantitative separation of intrinsic quenching from excitation-induced annihilation. Here, we address this ambiguity by directly correlating aggregate size, concentration, steady-state fluorescence intensity, and decay kinetics during controlled, incremental aggregation of isolated LHCII. By combining fluorescence correlation spectroscopy (FCS) with TCSPC in a unified experimental framework, we monitored structural and photophysical changes in real time as detergent removal drives biphasic aggregation. We quantified the aggregate composition from the particle concentrations, enabling direct scaling of the absorption cross-section with aggregate size. The average fluorescence lifetime decreased semi-logarithmically with increases in hydrodynamic radius, whereas steady-state fluorescence intensities deviated strongly from this trend. Intensitydependent measurements and steady-state kinetic modeling reveal that singlet-triplet annihilation (STA) emerges at moderate excitation intensities and rapidly becomes the dominant contributor to fluorescence quenching, even for relatively small aggregates. In contrast, intrinsic quenching increases more gradually with aggregate size. By quantitatively disentangling intrinsic excitation quenching from annihilation processes, this work demonstrates that STA can govern the apparent photophysical response of aggregated LHCII across excitation regimes commonly considered non-annihilating. The size-dependent mechanistic framework presented here provides a basis for distinguishing intrinsic quenching from annihilation effects in aggregation-based studies of photosynthetic antenna complexes.

physics.bio-ph↗

arXiv2024

Advanced analysis of single-molecule spectroscopic data

We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analysing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data -- such as fluorescence brightness, lifetime, and spectra -- of molecular- or nanometre-scale particles such as single dye molecules, quantum dots, or fluorescently labelled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI-based so it may be used without any programming knowledge. A multi-process architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.

physics.bio-ph↗

arXiv2024

Biophysics in Africa: challenges, priorities, and hopes

This report is a serious call to scientists, innovators, investors, and policymakers to invest in the development of biophysics in Africa. The complex problems of our day demand multidisciplinary approaches, and biophysics offers training in much-needed multi- and cross-disciplinary thinking. Biophysics is a research field at the forefront of modern science because it provides a powerful scientific platform that addresses many of the critical challenges humanity faces today and in the future. It is a vital source of innovation for any country interested in developing a high-tech economy. However, there is woefully little biophysics educational and research activity in Africa, representing a critical gap that must be addressed with urgency. This report suggests key research areas that African biophysicists should focus on, identifies major challenges to growing biophysics in Africa, and underscores the high-priority needs that must be addressed.

physics.soc-ph↗

arXiv2023

The African Biophysics Landscape: A Provisional Status Report

This is a provisional status report of biophysics activities in Africa. We start by highlighting the importance of biophysics research and development for every country's economy in the 21st century. Yet, the amount of biophysics activity in African countries varies between woefully little to nothing at all. We present a scope of biophysics research on the continent based on a pilot scientometrics study. We discuss a number of existing multinational programmes and infrastructure initiatives and propose a Pan African Professional Society for Biophysics. We emphasize the need for education, infrastructure and career development, and conclude with a list of suggested recommendations for expedited development of biophysics research on the continent.

physics.ed-ph↗

arXiv2022

Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective

Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. We then systematically discuss each of the core components of RT-FD-SPT in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. We then introduce a collection of metrics for RT-FD-SPT to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, we conclude with a discussion on future perspectives in the field.

physics.chem-ph↗

arXiv2022

Theoretical comparison of real-time feedback-driven single-particle tracking techniques

Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different RT-FD-SPT approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the Knight`s Tour (grid scan) method and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the Knight`s Tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.

physics.ins-det↗

arXiv2022

Plasmon resonances in multilayer Fanoshells

We develop a theoretical framework, based on a multipole, quasi-static approach, for the prediction of the localized surface plasmon resonances in Fanoshells formed via geometrical symmetry-breaking in multilayer nanoshells consisting of a metallic core, a dielectric inner shell, and a metallic outer shell. By tuning the core and shell offsets of a gold-silica-gold multilayer nanoshell, we show that the theoretical model is in good agreement with electrodynamic simulations. The dipolar resonances are more suppressed when the core and the outer shell are concurrently offset, and less suppressed when either the core, the inner shell, or the outer shell is offset. We attribute the former to coupling constants arising from dual symmetry-breaking, and the latter to coupling constants due to single symmetry-breaking. Using three performance parameters, we propose the outer shell offset as the optimal Fanoshell for sensing applications. This study systematically investigates all types of offset-based, symmetry-broken, metal-dielectric-metal multilayer nanoshells within the Rayleigh regime.

physics.optics↗

arXiv2020

Plasmonic Quantum Yield Enhancement of a Single Molecule Near a Nanoegg

We investigate the impact of the dipole-active modes formed via the mode-mixing of the dipole mode with higher-order surface plasmon modes of a nanoegg on the radiative decay rate and quantum yield of an excited molecule near the nanoegg. The Purcell factor, rate of power dissipation by the emitter, antenna efficiency of the nanoegg, as well as quantum yield enhancement of the emitter, were studied using the quasistatic approximation and the semiclassical theory of radiation, following the Gersten-Nitzan and Ford-Weber approaches. Compared to the concentric nanoshell, we show that the dielectric core-metallic shell nanoegg is a more efficient plasmonic nanoantenna for radiative decay rate enhancement of single emitters. The quantum yield of the emitter was found to be more enhanced near the nanoshell, while its emission rate was found to be more enhanced near the nanoegg.

physics.optics↗

arXiv2019

Strong plasmonic fluorescence enhancement of individual plant light-harvesting complexes

Plasmonic coupling of metallic nanoparticles and adjacent pigments can dramatically increase the brightness of the pigments due to the enhanced local electric field. Here, we demonstrate that the fluorescence brightness of a single plant light-harvesting complex (LHCII) can be significantly enhanced when coupled to single gold nanorods (AuNRs). The AuNRs utilized in this study were prepared via chemical reactions, and the hybrid system was constructed using a simple and economical spin-assisted layer-by-layer technique. Enhancement of fluorescence brightness of up to 240-fold was observed, accompanied by a 109-fold decrease in the average (amplitude-weighted) fluorescence lifetime from approximately 3.5 ns down to 32 ps, corresponding to an excitation enhancement of 63-fold and emission enhancement of up to 3.8-fold. This large enhancement is due to the strong spectral overlap of the longitudinal localized surface plasmon resonance of the utilized AuNRs and the absorption or emission bands of LHCII. This study provides an inexpensive strategy to explore the fluorescence dynamics of weakly emitting photosynthetic light-harvesting complexes at the single molecule level.

physics.bio-ph↗

arXiv2019

Localized Surface Plasmon Resonances of Simple Tunable Plasmonic Nanostructures

We derive and present systematic relationships between the analytical formulas for calculation of the localized surface plasmon resonances (LSPR) of some plasmonic nano-structures which we have categorized as simple. These relationships, including some new formulas, are summarized in a tree diagram which highlights the core-shell plasmons as the generators of solid and cavity plasmons. In addition, we show that the LSPR of complex structures can be reduced to that of simpler ones, using the LSPR of a nanorice as a case study, in the dipole limit. All the formulas were derived using a combination of the Drude model, the Rayleigh approximation, and the Fröhlich condition. The formulas are handy and they are in good agreement with the results of the plasmon hybridization theory. The formulas also account for dielectric effects, which provide versatility in the tuning of the LSPR of the nanostructures. A simplified model of plasmon hybridization is presented, allowing us to investigate the weak-coupling regimes of solid and cavity plasmons in the core-shell nanostructures we have studied.

physics.optics↗

arXiv2015

Design principles of natural light harvesting as revealed by single molecule spectroscopy

Biology offers a boundless source of adaptation, innovation, and inspiration. A wide range of photosynthetic organisms exist that are capable of harvesting solar light in an exceptionally efficient way, using abundant and low-cost materials. These natural light-harvesting complexes consist of proteins that strongly bind a high density of chromophores to capture solar photons and rapidly transfer the excitation energy to the photochemical reaction centre. The amount of harvested light is also delicately tuned to the level of solar radiation to maintain a constant energy throughput at the reaction centre and avoid the accumulation of the products of charge separation. In this Review, recent developments in the understanding of light harvesting by plants will be discussed, based on results obtained from single molecule spectroscopy studies. Three design principles of the main light-harvesting antenna of plants will be highlighted: (a) fine, photoactive control over the intrinsic protein disorder to efficiently use intrinsically available thermal energy dissipation mechanisms; (b) the design of the protein microenvironment of a low-energy chromophore dimer to control the amount of shade absorption; (c) the design of the exciton manifold to ensure efficient funneling of the harvested light to the terminal emitter cluster.

q-bio.BM↗